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Abstract

An accurate reconstruction of the eukaryotic tree of life is essential to identify the innovations
underlying the diversity of microbial and macroscopic (e.g. plants and animals) eukaryotes.
Previous work has divided eukaryotic diversity into a small number of high-level ‘supergroups’,
many of which receive strong support in phylogenomic analyses. However, the abundance of
data in phylogenomic analyses can lead to highly supported but incorrect relationships due to
systematic phylogenetic error. Further, the paucity of major eukaryotic lineages (19 or fewer)
included in these genomic studies may exaggerate systematic error and reduces power to
evaluate hypotheses. Here, we use a taxon-rich strategy to assess eukaryotic relationships. We
show that analyses emphasizing broad taxonomic sampling (up to 451 taxa representing 72
major lineages) combined with a moderate number of genes yield a well-resolved eukaryotic tree
of life. The consistency across analyses with varying numbers of taxa (88-451) and levels of
missing data (17-69%) supports the accuracy of the resulting topologies. The resulting stable
topology emerges without the removal of rapidly evolving genes or taxa, a practice common to
phylogenomic analyses. Several major groups are stable and strongly supported in these
analyses (e.g. SAR, Rhizaria, Excavata), while the proposed supergroup ‘Chromalveolata’ is
rejected. Further, extensive instability among photosynthetic lineages suggests the presence of
systematic biases including endosymbiotic gene transfer from symbiont (nucleus or plastid) to
host. Our analyses demonstrate that stable topologies of ancient evolutionary relationships can
be achieved with broad taxonomic sampling and a moderate number of genes. Finally, taxonrich
analyses such as presented here provide a method for testing the accuracy of relationships
that receive high bootstrap support in phylogenomic analyses and enable placement of the
multitude of lineages that lack genome scale data.

Our understanding of the eukaryotic tree of life and the tremendous diversity of microbial eukaryotes is in flux as additional genes and diverse taxa are sampled for molecular analyses. Despite instability in many analyses, ...

Microbial ecology is plagued by problems of an abstract nature. Cell sizes are so small and population sizes so large that both are virtually incomprehensible. Niches are so far from our everyday experience as to make their ...

Perspectives on the classification of eukaryotic diversity have changed rapidly in recent years, as the four eukaryotic
groups within the five-kingdom classification—plants, animals, fungi, and protists—have been transformed ...

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